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Question: "GOplot" and problem with making an integrated matrix
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Hi everybody!

Recently I became familiar with a new Gene Ontology plotting library in R called "GOplot". There is a tutorial in the developer site but from the very first point i have some problems with it. I put the tutorial in this question so you can review it: http://wencke.github.io/

1) There is no function in R like:

 install.github('wencke/wencke.github.io')

2) If you skip this part you go through making dataframes. I don't know how to make mentioned dataframes in toy example part of tutorial for my microarray analysis. I would be really appreciate if you can help me with the second problem specially.

Thanks a lot.

ADD COMMENTlink 20 months ago farzaneafzali • 50 • updated 20 months ago zx8754 7.5k
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Hi farzaneafzali I am facing the same problem. Did you figure out how to solve it. Thanks, Hossam

ADD REPLYlink 16 months ago
hel226
• 0
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What exactly is the problem, please clarify.

ADD REPLYlink 16 months ago
zx8754
7.5k
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Thank you zx8754 for kind concern. I am beginner with R and i can load my data as .CSV file but the developers are using .rda format which i cannot created i have hard time to do this, can you help me?

ADD REPLYlink 14 months ago
hel226
• 0
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They are just R data file formats, once you read them in they become R objects. Then you can compare with your CSV files. Please see for more info:

ADD REPLYlink 14 months ago
zx8754
7.5k
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Thank you so much it worked!

ADD REPLYlink 14 months ago
hel226
• 0
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Hi and sorry for the late reply. Recently, I have updated my R version into 3.5 and then updated all my packages. Then, the installation process took place. But, I still have problem with making

circ <- circle_dat(EC$david, EC$genelist)

out of my data. It gives me this error:

Error in `$<-.data.frame`(`*tmp*`, "genes", value = character(0)) : 
  replacement has 0 rows, data has 2203

I will post my problem as the new question now.

ADD REPLYlink 12 months ago
farzaneafzali
• 50
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  1. You have a typo, try: devtools::install_github("wencke/wencke.github.io"), note that you need to have devtools package installed.

  2. Data is within the package, you get them as noted in the tutorial data(EC), it is a list of dataframes.

The toy example
GOplot comes with a manually compiled data set....

ADD COMMENTlink 20 months ago zx8754 7.5k
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Hello, I am trying to run GOplot with R. I was able to import my data and make the initial figures. However, when I run the last command (pasted below): I get an error message. Could anyone help me to solve this problem?

circ <- circle_dat(david, genelist) genes <- genes process <- process chord <- chord_dat(circ, genes, process) chord <- chord_dat(data = circ, genes = genes, process = process) GOChord(chord, space = 0.02, gene.order = 'logFC', gene.space = 0.25, gene.size = 5)

I get this error message. Error in $<-.data.frame(*tmp*, "x.start", value = c(0, 0.133335565891055, : replacement has 52 rows, data has 46

Please, zx8754 could you help me with this problem?

ADD REPLYlink 14 months ago
yatta.b
• 10
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This is a popular error message, see:

If this doesn't help you to solve your issue, post a new question (not a comment).

ADD REPLYlink 14 months ago
zx8754
7.5k
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Thank you very much!

ADD REPLYlink 14 months ago
yatta.b
• 10
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Thanks Z I know where TOY DATA is :D I just want to make one of them for myself. enfact in know the code for making dataframe out of my data but it gives me an error when i want to proceed with this code

circ <- circle_dat(go, tn)

This is the code i use for entering the excel files into R and make them datafarme:

go <- data.frame(read.xlsx(file.choose(), colNames=TRUE))

ADD REPLYlink 20 months ago
farzaneafzali
• 50
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Then load the toy data, and make your own, and compare the output of str().

ADD REPLYlink 20 months ago
zx8754
7.5k

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